Influenza, or the flu, is a contagious viral infection of the respiratory tract. Transmission of influenza is primarily airborne (i.e., coughing or sneezing); the peak of transmission usually occurs in the winter months. Symptoms commonly include fever, chills, headache, muscle aches, malaise, cough, and sinus congestion. Gastrointestinal symptoms (i.e., nausea, vomiting, or diarrhea) may also occur, primarily in children, but are less common in adults. Symptoms generally appear within two days of exposure to an infected person. Pneumonia may develop as a complication of influenza infection, causing increased morbidity and mortality in pediatric, elderly, and immunocompromised populations. Influenza viruses are classified into types A, B, and C, the former two of which cause most human infections. Influenza A is the most common type of influenza virus in humans, and is generally responsible for seasonal flu epidemics and occasionally for pandemics. Influenza A viruses can also infect animals such as birds, pigs, and horses. Infections with influenza B virus are generally restricted to humans and are less frequent causes of epidemics. Influenza A viruses are further divided into subtypes on the basis of two surface proteins: hemagglutinin (H) and neuraminidase (N). Seasonal flu is normally caused by subtypes H1, H2, H3, and N1 and N2. In addition to seasonal flu, a novel H1N1 strain was identified in humans in the United States in early 2009.
Respiratory syncytial virus (RSV), a member of the Paramyxoviridae family consisting of two strains (subgroups A and B), is also the cause of a contagious disease that afflicts primarily infants and the elderly who are immune-compromised, e.g., chronic lung or heart disease or undergoing treatment for conditions that reduces the strength of their immune system. The virus can live for hours on countertops and toys and cause both upper respiratory infections, such as colds, and lower respiratory infections manifesting as bronchiolitis and pneumonia.4 By the age of two, most children have already been infected by RSV, but because only weak immunity develops, both children and adults can become reinfected. Symptoms usually appear four to six days after infection. The disease is typically self-limiting, lasting about one to two weeks in infants. In adults, the infection lasts about five days and presents with symptoms consistent with a cold, such as rhinorrhea, fatigue, headache, and fever. The RSV season overlaps with influenza season somewhat as infections begin to rise during the fall and continue through early spring. RSV infections, however, also occur at other times of the year, although rarely.
Active surveillance programs in conjunction with infection control precautions are important components for preventing transmission of influenza and RSV. The use of assays providing rapid results to identify patients infected with these seasonal infections is also an important factor for effective control, proper choice of treatment, and prevention of widespread outbreaks.
The genome of influenza viruses comprises eight RNA segments of 0.9-2.3 kb that together span approximately 13.5 kb and encode 11 proteins. These 8 segments designated PB2, PB1, PA, HA, NP, NA, MP and NS are under constant selective pressure which leads to rapid sequence changes (antigenic drift). In addition to changes on the sequence level Influenza A has the ability to exchange whole segments with other Influenza A viruses (antigenic shift). This process leads to the emergence of pandemic influenza strains (i.e. Influenza A H1N1pdm09, swing origin H3N2).
The two proteins, hemagglutinin (HA) and neuraminidase (NA) determine the subtypes (H and N, respectively) of Influenza A virus. There are 16 H subtypes and 9 N subtypes. The H1N1 and H3N2 subtypes cause the vast majority of influenza infections in humans. Influenza B virus has a similar structure of RNA segments; however the Flu B viruses do not have subtypes.
This constant antigenic drift and antigenic shift makes it difficult to maintain influenza detection assays from season to season. There remains a need for a robust influenza detection assay that will remain accurate even as the influenza genome undergoes genetic drift.